LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 4.0469995588064185*${_u_distance} variable lattice_constant_converted equal 4.0469995588064185*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 25.913440963873423*${_u_distance} variable xmax_converted equal 25.913440963873423*1 variable ymin_converted equal -51.830928927305656*${_u_distance} variable ymin_converted equal -51.830928927305656*1 variable ymax_converted equal 51.830928927305656*${_u_distance} variable ymax_converted equal 51.830928927305656*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 4.0469995588064185*${_u_distance} variable zmax_converted equal 4.0469995588064185*1 lattice fcc ${lattice_constant_converted} lattice fcc 4.04699955880642 Lattice spacing in x,y,z = 4.047 4.047 4.047 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.9134409638734 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.9134409638734 -51.8309289273057 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 25.9134409638734 -51.8309289273057 51.8309289273057 ${zmin_converted} ${zmax_converted} units box region whole block 0 25.9134409638734 -51.8309289273057 51.8309289273057 0 ${zmax_converted} units box region whole block 0 25.9134409638734 -51.8309289273057 51.8309289273057 0 4.04699955880642 units box create_box 2 whole Created orthogonal box = (0 -51.8309 0) to (25.9134 51.8309 4.047) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 51.8309289273057 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 -4 0 orient y 4 5 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 5 -4 0 orient y 4 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68832 5.68832 4.047 create_atoms 1 region upper Created 329 atoms create_atoms CPU = 0.000179052 secs group upper type 1 329 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 2.881405906844782 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -51.8309289273057 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 5 4 0 orient y -4 5 0 orient z 0 0 1 lattice fcc 4.04699955880642 orient x 5 4 0 orient y -4 5 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.68832 5.68832 4.047 create_atoms 2 region lower Created 329 atoms create_atoms CPU = 7.48634e-05 secs group lower type 2 329 atoms in group lower displace_atoms lower move -2.881405906844782 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style meam/c pair_coeff * * ./SM_871795249052_000-files/b'library.NAlTi' N Al Ti ./SM_871795249052_000-files/b'meam.NAlTi' Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*4.04699955880642 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 2.02349977940321 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) pair meam/c, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Deleted 10 atoms, new total = 648 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 8 30 2 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 11.37 | 11.37 | 11.37 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2157.1368 0 -2157.1368 1663.2899 196 0 -2170.6346 0 -2170.6346 -5758.4588 Loop time of 3.16162 on 1 procs for 196 steps with 648 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2157.13678339 -2170.63460924 -2170.63460924 Force two-norm initial, final = 19.0854 9.92126e-06 Force max component initial, final = 5.13238 2.36205e-06 Final line search alpha, max atom move = 1 2.36205e-06 Iterations, force evaluations = 196 384 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1461 | 3.1461 | 3.1461 | 0.0 | 99.51 Neigh | 0.0014689 | 0.0014689 | 0.0014689 | 0.0 | 0.05 Comm | 0.0082746 | 0.0082746 | 0.0082746 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005765 | | | 0.18 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4477 ave 4477 max 4477 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27624 ave 27624 max 27624 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55248 ave 55248 max 55248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55248 Ave neighs/atom = 85.2593 Neighbor list builds = 1 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 11.38 | 11.38 | 11.38 Mbytes Step Temp E_pair E_mol TotEng Press Volume 196 0 -2170.6346 0 -2170.6346 -5758.4588 10871.194 1196 0 -2170.746 0 -2170.746 -1239.6528 10806.879 Loop time of 17.4094 on 1 procs for 1000 steps with 648 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2170.63460924 -2170.74603268 -2170.74603268 Force two-norm initial, final = 49.6667 0.00249989 Force max component initial, final = 40.4712 0.0016855 Final line search alpha, max atom move = 0.807388 0.00136085 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.228 | 17.228 | 17.228 | 0.0 | 98.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.042411 | 0.042411 | 0.042411 | 0.0 | 0.24 Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1385 | | | 0.80 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4473 ave 4473 max 4473 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27648 ave 27648 max 27648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55296 ave 55296 max 55296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55296 Ave neighs/atom = 85.3333 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal 0.0 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 8 30 2 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (4) compute pair/local, occasional, copy from (2) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 10.25 | 10.25 | 10.25 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2170.746 0 -2170.746 -1239.6528 Loop time of 2.14577e-06 on 1 procs for 0 steps with 648 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.146e-06 | | |100.00 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4481 ave 4481 max 4481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27684 ave 27684 max 27684 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55368 ave 55368 max 55368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55368 Ave neighs/atom = 85.4444 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 10.25 | 10.25 | 10.25 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2170.746 -2170.746 25.872834 103.66186 4.0293713 -1239.6528 -1239.6528 -0.24949194 -3718.607 -0.10200452 2.4460114 315.12932 Loop time of 9.53674e-07 on 1 procs for 0 steps with 648 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4481 ave 4481 max 4481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27684 ave 27684 max 27684 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55368 ave 55368 max 55368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55368 Ave neighs/atom = 85.4444 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_077.3196/numatoms.out 648 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2170.74603268271-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2170.74603268271-648*${isolated_atom_energy} variable adjusted_pe_metal equal -2170.74603268271-648*0 print "${adjusted_pe_metal} eV" file output/dump_077.3196/energy.out -2170.74603268271 eV print "${mindist_metal} Angstroms" file output/dump_077.3196/mindistance.out 2.44601136549383 Angstroms write_dump all cfg output/dump_077.3196/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_077.3196/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:20